--- trunk/OOPSE/utils/sysbuilder/Makefile.in	2003/10/24 22:01:24	820
+++ trunk/OOPSE/utils/sysbuilder/Makefile.in	2003/10/24 22:17:45	821
@@ -4,7 +4,7 @@ TOP=../..
 # You should not change anything here.              #
 #####################################################
 
-TOP=../..
+TOP=@abs_top_builddir@
 
 .SUFFIXES : .cpp .c $(O)
 
@@ -112,28 +112,30 @@ INCLUDES= -I.. -I../../../libBASS -I../../../libmdtool
 
 # include paths starting with "." are all relative to the SUBDIRS!!!
 
-INCLUDES= -I.. -I../../../libBASS -I../../../libmdtools
-MPI_INCLUDES= $(MPI_INC) $(MPI_INC)/mpi2c++ 
+INCLUDES= -I.. -I$(TOP)/libBASS -I$(TOP)/libmdtools
 CFLAGS=$(CFLAGS_C) $(INCLUDES) $(DECLARES)
 CXXFLAGS=$(CXXFLAGS_C) $(INCLUDES) $(DECLARES)
-DEPFLAGS=$(CFLAGS_C) -I. $(SPRNG_INC) $(MPI_INCLUDES) -I../../libBASS -I../../libmdtools
-MPI_CXXFLAGS=$(CXXFLAGS) $(MPI_INCLUDES) $(MPI_DECLARES)
+DEPFLAGS=$(CFLAGS_C) -I. $(SPRNG_INC) -I$(TOP)/libBASS -I$(TOP)/libmdtools
 
 
 SYSBUILD=sysBuild$(EXE)
+BUILDER_LIB=libBuilder.a
+LBILAYER=latticeBilayer$(EXE)
 
 BASS_LIB=$(TOP)/libBASS/libBASS.a
-BASS_MPI_LIB=$(TOP)/libBASS/libBASS_MPI.a
 MD_LIB=$(TOP)/libmdtools/libmdtools.a
-MD_MPI_LIB=$(TOP)/libmdtools/libmdtools_MPI.a
 LIBS=$(BASS_LIB) $(MD_LIB)
-MPI_LIBS=$(BASS_MPI_LIB) $(MD_MPI_LIB)
 
-SYSBUILD_LDFLAGS=-L$(TOP)/libBASS -L$(TOP)/libmdtools -L$(SPRNG_LIBDIR)
-SYSBUILD_LDADD=-lmdtools -lBASS $(SPRNG_LIB) $(F90LIBS)
+#SYSBUILD_LDFLAGS=-L$(TOP)/libBASS -L$(TOP)/libmdtools -L$(SPRNG_LIBDIR)
+#SYSBUILD_LDADD=-lmdtools -lBASS $(SPRNG_LIB) $(F90LIBS)
 
+
 SRC_DIR := $(PWD)
 
+LBILAYER_LDFLAGS=-L$(TOP)/libBASS -L$(TOP)/libmdtools -L$(SPRNG_LIBDIR) -L$(SRC_DIR)
+LBILAYER_LDADD=-lBuilder -lmdtools -lBASS $(SPRNG_LIB) $(F90LIBS)
+
+
 PREFS=-DOOPSE_HOME=\"$(OOPSE_HOME)\" 
 
 obj/%.o: %.cpp
@@ -150,83 +152,111 @@ SYSBUILD_C_FILES = $(DIR)/cmdline.c
 
 # sysBuilder files
 
-SYSBUILD_C_FILES = $(DIR)/cmdline.c
-SYSBUILD_CXX_FILES = \
-	$(DIR)/sysBuild.cpp \
-	$(DIR)/bilayerSys.cpp \
+#SYSBUILD_C_FILES = $(DIR)/cmdline.c
+#SYSBUILD_CXX_FILES = \
+#	$(DIR)/sysBuild.cpp \
+#	$(DIR)/bilayerSys.cpp \
+#	$(DIR)/MoLocator.cpp \
+#	$(DIR)/latticeBuilder.cpp \
+#	$(DIR)/nanoBuilder.cpp
+
+#latticeBilayer files
+
+LBILAYER_CXX_FILES = $(DIR)/latticeBilayer.cpp
+
+# libBuilder files
+
+BUILDER_LIB_CXX_FILES = \
 	$(DIR)/MoLocator.cpp \
-	$(DIR)/latticeBuilder.cpp \
-	$(DIR)/nanoBuilder.cpp
+	$(DIR)/QuickBass.cpp \
+	$(DIR)/latticeBuilder.cpp
 
+
 # the sources
 
 DIR:=.
 
-SYSBUILD_C_SRCS := $(SYSBUILD_C_FILES)
-SYSBUILD_CXX_SRCS := $(SYSBUILD_CXX_FILES)
-SYSBUILD_SRCS := $(SYSBUILD_C_SRCS) $(SYSBUILD_CXX_SRCS)
+#SYSBUILD_C_SRCS := $(SYSBUILD_C_FILES)
+#SYSBUILD_CXX_SRCS := $(SYSBUILD_CXX_FILES)
+#SYSBUILD_SRCS := $(SYSBUILD_C_SRCS) $(SYSBUILD_CXX_SRCS)
 
-C_CXX_SRCS :=  $(SYSBUILD_C_SRCS) $(SYSBUILD_CXX_SRCS)
+LBILAYER_CXX_SRCS := $(LBILAYER_CXX_FILES)
+LBILAYER_SRCS := $(LBILAYER_CXX_SRCS)
 
+BUILDER_LIB_CXX_SRCS := $(BUILDER_LIB_CXX_FILES)
+BUILDER_LIB_SRCS := $(BUILDER_LIB_CXX_SRCS)
+
+C_CXX_SRCS :=  $(LBILAYER_SRCS) $(BUILDER_LIB_SRCS)
+
+C_SRCS :=
+CXX_SRCS := $(LBILAYER_CXX_SRCS) $(BUILDER_LIB_CXX_SRCS)
+
 #the objects
 
 DIR:=obj
 
-SYSBUILD_C_OBJS := $(SYSBUILD_C_FILES:.c=.o)
-SYSBUILD_CXX_OBJS := $(SYSBUILD_CXX_FILES:.cpp=.o)
-SYSBUILD_OBJS := $(SYSBUILD_C_OBJS) $(SYSBUILD_CXX_OBJS)
+#SYSBUILD_C_OBJS := $(SYSBUILD_C_FILES:.c=.o)
+#SYSBUILD_CXX_OBJS := $(SYSBUILD_CXX_FILES:.cpp=.o)
+#SYSBUILD_OBJS := $(SYSBUILD_C_OBJS) $(SYSBUILD_CXX_OBJS)
 
-DIR:=MPIobj
+LBILAYER_CXX_OBJS := $(LBILAYER_CXX_FILES:.cpp=.o)
+LBILAYER_OBJS := $(LBILAYER_CXX_OBJS)
 
-SYSBUILD_C_MPIOBJS := $(SYSBUILD_C_FILES:.c=.o)
-SYSBUILD_CXX_MPIOBJS := $(SYSBUILD_CXX_FILES:.cpp=.o)
-SYSBUILD_MPIOBJS := $(SYSBUILD_C_MPIOBJS) $(SYSBUILD_CXX_MPIOBJS)
+BUILDER_LIB_CXX_OBJS := $(BUILDER_LIB_CXX_FILES:.cpp=.o)
+BUILDER_LIB_OBJS := $(BUILDER_LIB_CXX_OBJS)
 
 LIBSUBDIRS = \
-	obj \
-	MPIobj
+	obj
 
-all : $(SYSBUILD)
+all : $(BUILDER_LIB) $(LBILAYER)
 
 depend: Make.dep
 
-sysBuild$(EXE) : $(SYSBUILD_OBJS) $(BASS_LIB) $(MD_LIB)
-	$(CXX) $(CXXFLAGS) $(SYSBUILD_OBJS) -o $@ $(SYSBUILD_LDFLAGS) $(SYSBUILD_LDADD)
+#sysBuild$(EXE) : $(SYSBUILD_OBJS) $(BASS_LIB) $(MD_LIB)
+#	$(CXX) $(CXXFLAGS) $(SYSBUILD_OBJS) -o $@ $(SYSBUILD_LDFLAGS) $(SYSBUILD_LDADD)
 
-install : $(SYSBUILD) 
+libBuilder.a: $(BUILDER_LIB_OBJS)
+	$(RM) $@
+	$(AR) cr $@ $(BUILDER_LIB_OBJS)
+	$(RANLIB) $@
+
+latticeBilayer$(EXE): $(LBILAYER_OBJS) $(BUILDER_LIB)  $(BASS_LIB) $(MD_LIB)
+	$(CXX) $(CXXFLAGS) $(LBILAYER_OBJS) -o $@ $(LBILAYER_LDFLAGS) $(LBILAYER_LDADD)
+
+install : $(LBILAYER) 
 	$(MKINSTALLDIRS) $(OOPSE_HOME)/bin
-	$(INSTALL_PROGRAM) -s $(SYSBUILD) $(OOPSE_HOME)/bin/$(SYSBUILD)
+	$(INSTALL_PROGRAM) -s $(LBILAYER) $(OOPSE_HOME)/bin/$(LBILAYER)
 
 
 tests : dummy
 
 
-$(OOPSE_HOME)/bin/$(SYSBUILD) : $(SYSBUILD)
+$(OOPSE_HOME)/bin/$(LBILAYER) : $(LBILAYER)
 	$(MAKE) install
 
-links : $(OOPSE_HOME)/bin/$(SYSBUILD)  
+links : $(OOPSE_HOME)/bin/$(LBILAYER)  
 	$(MKINSTALLDIRS) $(PREFIX)/bin
-	cd $(PREFIX)/bin; $(LN_S) -f $(OOPSE_HOME)/bin/$(SYSBUILD) $(SYSBUILD)
+	cd $(PREFIX)/bin; $(LN_S) -f $(OOPSE_HOME)/bin/$(LBILAYER) $(LBILAYER)
 
 clean : dummy
 	for i in $(LIBSUBDIRS); do \
 	  (cd $$i; $(RM) *.o) || exit 1; \
 	done
-	$(RM) $(SYSBUILD) *.o *~ Make.temp
+	$(RM) $(LBILAYER) $(BUILDER_LIB) *.o *~ Make.temp
 
 distclean : dummy
 	for i in $(LIBSUBDIRS); do \
 	  (cd $$i; $(RM) *.o) || exit 1; \
 	done
-	$(RM) $(SYSBUILD) *.o *~ Make.temp
+	$(RM) $(LBILAYER) $(BUILDER_LIB) *.o *~ Make.temp
 
 devclean : distclean
 
 Make.dep : 
 	echo "# DO NOT DELETE THIS LINE - used by make depend" > Make.dep
-	$(CC) $(DEPFLAGS) -MM $(SYSBUILD_C_SRCS) \
+	$(CC) $(DEPFLAGS) -MM $(C_SRCS) \
 		| sed 's/\.o:/\$$(O)\ :/g' > Make.temp
-	$(CXX) $(DEPFLAGS) -MM $(SYSBUILD_CXX_SRCS) \
+	$(CXX) $(DEPFLAGS) -MM $(CXX_SRCS) \
 		| sed 's/\.o:/\$$(O)\ :/g' >> Make.temp
 	cat Make.temp | sed 's/^[a-zA-Z0-9]/obj\/&/g' >> Make.dep
 	cat Make.temp | sed 's/^[a-zA-Z0-9]/MPIobj\/&/g' >> Make.dep